Contacts of the strand formed by residues 4 - 11 (chain A) in PDB entry 5FSJ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 4 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A GLY* 1.3 73.0 - - - -
5A SER* 1.3 67.9 + - - +
6A THR* 3.5 8.3 + - + +
23A THR* 3.4 4.0 - - - -
24A TYR* 2.9 50.9 + - + +
33A ASN* 4.8 0.2 - - - -
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Residues in contact with SER 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A GLY 4.3 0.6 + - - -
4A THR* 1.3 79.1 + - - +
6A THR* 1.3 64.7 + - - +
22A THR 3.6 8.3 - - - -
33A ASN* 3.0 32.9 + - - +
34A THR* 5.4 9.8 - - - +
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Residues in contact with THR 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A THR* 3.6 15.5 - - + +
5A SER* 1.3 79.6 - - - +
7A VAL* 1.3 69.7 + - - +
21A ASN* 3.6 5.7 + - - +
22A THR* 2.7 52.3 + - - +
23A THR 3.5 3.5 + - - -
24A TYR* 3.7 21.7 + - + -
28A TYR* 3.8 10.2 - - + -
60A ASN* 4.0 9.4 - - - -
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Residues in contact with VAL 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A THR* 1.3 80.1 - - - +
8A GLY* 1.3 71.2 + - - +
19A ASN* 3.9 25.6 - - + +
20A ILE 3.5 6.1 - - - +
21A ASN* 4.1 15.5 - - - +
60A ASN* 3.2 10.6 + - - +
61A GLN* 5.7 0.7 + - - -
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Residues in contact with GLY 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A VAL* 1.3 79.3 - - - +
9A VAL* 1.3 63.3 + - - +
19A ASN* 3.3 6.4 - - - +
20A ILE* 2.8 40.2 + - - -
22A THR* 3.7 3.0 + - - -
60A ASN* 3.2 29.1 - - - +
61A GLN* 5.2 0.9 - - - -
62A PHE* 4.6 0.9 - - - -
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Residues in contact with VAL 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A GLY* 1.3 75.4 - - - +
10A GLY* 1.3 61.8 + - - +
17A GLN* 3.6 37.5 - - + +
18A LYS 3.5 8.5 - - - +
19A ASN* 3.7 13.7 - - - +
20A ILE* 4.4 1.5 - - - +
60A ASN 3.2 3.0 + - - -
61A GLN* 2.7 37.5 - - - +
62A PHE* 2.8 25.9 + - - -
63A PHE* 3.6 10.3 - - + -
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Residues in contact with GLY 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A VAL* 1.3 78.0 - - - +
11A ARG* 1.3 60.9 + - - -
12A GLY 4.3 0.2 - - - -
17A GLN* 3.2 7.6 - - - +
18A LYS 2.9 33.2 + - - -
20A ILE* 4.9 1.2 - - - +
62A PHE* 3.2 21.8 - - - -
63A PHE* 3.9 8.5 - - - -
71A VAL* 4.5 8.5 - - - -
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Residues in contact with ARG 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A GLY* 1.3 75.0 - - - +
12A GLY* 1.3 64.0 + - - +
15A GLY* 3.3 40.5 + - - +
16A ASP 3.2 4.5 - - - +
17A GLN* 4.0 16.0 + - - +
62A PHE 3.0 12.1 + - - +
63A PHE* 3.3 55.4 + - + +
64A ALA 5.3 0.7 - - - +
68A ALA* 3.4 19.6 - - - +
71A VAL* 3.8 6.9 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il